When AE2 allocates an item to a storage container, it can be thought to do the following tasks in the following order:
The system analyzes all storage components on the network that will allow the item (that is, it excludes containers with the item blacklisted and containers that cannot fit the item) and compiles a list sorted by priority.
If any of the storage containers in the list contain the item already or have the item explicitly whitelisted[citation needed], all storage containers that don't are removed from the list. This includes individual cells in ME Drives.
Picks the highest-priority container of the list and selects it as the destination.
If there is a tie, a container is picked using information that is not readily available to the player[citation needed]. Avoid duplicate priorities to avoid this problem.
If the destination is an ME drive that contains multiple valid destination cells, it reads it like a book, picking the first valid cell it comes across.
The item is moved to the destination cell or container. If there are leftovers of the item (say, the container couldn't accommodate the whole stack), the process is repeated again with those excess items.
That is to say, it is completely, rigidly algorithmic. You'll have to manually partition drives and defragment them yourself. Or, of course, you could automate defragging using an I/O Port and some tube wizardry.